Devteam: On 10/23 an update was posted to package_picard_1_56_0 that breaks tool Picard. Since 10/23, picard depends on package_picard_1_56_0, which in turn depends on picard 1.122.0, but that dependency makes absolutely no sense. Now when I run PairedReadMateFixer I get: #################### ## exit code=1; stdout= Error: Unable to access jarfile /FixMateInformation.jar #################### which appears to be caused by bad paths I don't understand toolshed logic for revisions: when I install tools with very specific revisions, the tool depends on very specific revisions of other tools. However, when I install a tool that depends on a package_*, the package has revision information, but it is ignored in favor of installing the LATEST revision of the package. If someone posts a buggy revision of a package_* to the toolshed, there is no way to avoid installing it until a fixed version is posted in its place. For example, when I run: python ./scripts/api/install_tool_shed_repositories.py --api XXXXXXXXXX --local http://127.0.0.1:8080 --url http://toolshed.g2.bx.psu.edu --name package_picard_1_56_0 --owner devteam --revision 61e41d21cb6f --tool-deps --repository-deps --panel-section-name "Other (Main Tool Shed)"' I expect package_picard_1_56_0:61e41d21cb6f to be installed, but instead I get package_picard_1_56_0:4a49481f29e7: ####### Response -------- /api/tool_shed_repositories/03501d7626bd192f name: package_picard_1_56_0 status: Installed tool_shed_status: {u'latest_installable_revision': u'True', u'revision_update': u'False', u'revision_upgrade': u'False', u'repository_deprecated': u'False'} deleted: False ctx_rev: 1 error_message: dist_to_shed: False tool_shed: toolshed.g2.bx.psu.edu installed_changeset_revision: 4a49481f29e7 uninstalled: False owner: devteam changeset_revision: 4a49481f29e7 id: 03501d7626bd192f includes_datatypes: False ####### Why ignore the package revisions? Btw, I did find an alternate (and working) package_picard_1_56_0 in the test toolshed, but why do I need to depend on the test toolshed for a production environment? -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan@msi.umn.edu boll0107@umn.edu